tbuckley/cabot-search huggingface dataset:
Abstract 2012: A humanized anaplastic lymphoma kinase (ALK)-directed antibody-drug conjugate (ADC) demonstrates potent cytotoxicity in neuroblastoma (NBL) and fusion positive rhabdomyosarcoma (FP RMS)
Authors: Alberto D. Guerra, Annie Kennedy, Cynthia Adams, Rawan Shraim, Amber K. Weiner, Chuan Chen, Kateryna Krytska, Colleen Larmour, Smita Matkar, Dimiter Dimitrov, Dontcho V. Jelev, Yael P. Mossé
Journal: Cancer Research (2022)

Abstract Introduction: ALK is a lineage restricted oncoprotein expressed on the cell surface of NBL as wild-type (WT), mutated, or amplified, and recently shown to be overexpressed in FP RMS. Small molecule inhibitors have shown potent efficacy in NBL with ALK mutations or amplifications, but is limited to a minority of the high-risk population and have demonstrated conferred resistance. We have previously shown the potential of an ADC approach for WT ALK-expressing NBL with a chimeric ALK-directed ADC CDX-0125. Methods: A highly specific humanized ALK antibody KTN0239 was developed with site-specific conjugation of an amine-azido linker conjugated to pyrrolobenzodiazepine (PBD) dimers or duocarmycin using click chemistry. ALK surface expression in ALK amplified (NB-1), WT non-amplified (IMR-32), mutant (Felix, SH-SY5Y, Kelly, NB1-643), and WT null (SK-N-AS) cell lines were quantified with flow cytometry using the primary KTN0239 antibody. Internalization kinetics of KTN0239 were measured using Incucyte® Fabflour-pH labeling. In vitro ADC IC50 values and viability rescue were assessed with a CellTiter-Glo® assay with ADC concentrations ranging from 10 fM to 10 nM. Western blot was used to elucidate cytotoxic mechanism of the ADC. Results: ALK surface protein molecule expression was 21,820 in NB-1 cells, 3,708 in Felix, and 1,426 in SK-N-AS cells. KTN0239 was internalized into NB1 cells with a logarithmic trend, with &amp;gt;65% of antibody internalized within 8 hours. NB-1 cell line viability was rescued to &amp;gt;80% when 2.5 nM of KTN0239 was in competition with the PBD-conjugated ADC at the IC50 concentration. The ADC induced activation of PARP, caspase-3, and γH2AX without attenuation of ALK signaling in NB-1 cells. Conclusions: ADCs directed to ALK-expressing cancers are a promising therapeutic approach. The efficacy of the ADCs are currently being tested in NBL and FP RMS mouse models, and will be reported. Mean IC50 values (pM) of ADCs with a drug antibody ratio (DAR) of 6 in NBL cell lines ADC: PBD-conjugated Duocarmycin-conjugated NB-1 14 71 IMR-32 12 741 Felix 51 110 NB-1643 6.6 1,196 Kelly 517 34,700 SH-SY5Y 693 3,024 SK-N-AS 533 1,420 Citation Format: Alberto D. Guerra, Annie Kennedy, Cynthia Adams, Rawan Shraim, Amber K. Weiner, Chuan Chen, Kateryna Krytska, Colleen Larmour, Smita Matkar, Dimiter Dimitrov, Dontcho V. Jelev, Yael P. Mossé. A humanized anaplastic lymphoma kinase (ALK)-directed antibody-drug conjugate (ADC) demonstrates potent cytotoxicity in neuroblastoma (NBL) and fusion positive rhabdomyosarcoma (FP RMS) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2012.
Abstract 2692: Identification of functional single nucleotide polymorphisms in cryptic exon 3 of the androgen receptor gene
Authors: Jasper Van Goubergen, Florian Handle, Marcus V. Cronauer, Frédéric R. Santer
Journal: Cancer Research (2022)

Abstract Castration resistant prostate cancer (CRPC) involves the upregulation of androgen receptor variants (AR-Vs), of which AR-V7 is clinically the most relevant. By lacking the ligand-binding domain, AR-V7 is constitutively active and may therefore bypass AR signaling inhibitors. Treating CRPC involves improved AR signaling inhibitors or taxane-based chemotherapy. However, the optimal treating sequence may differ from patient to patient. The presence of AR-V7 in the nucleus of circulating PCa cells, which is associated with AR targeted therapy resistance, is used as a therapy-guiding biomarker. This stratification has a high predictive power and specificity, but its sensitivity is unsatisfying and can only be done by highly specialized laboratories. A PCR/sequencing based test would improve the sensitivity of this biomarker, but it requires a better understanding of AR-V7’s functional regulation. Therefore, we aim here to analyze single nucleotide polymorphisms (SNPs) in the 3’ untranslated region (UTR) of AR-V7 that might have an impact on AR-V7’s expression and/or functional activity. The LD trait tool of NIH was used to search for trait association with AR cryptic exon (CE3) SNPs. Four RNA binding motif databases (oRNAment, ATtRACT, RBP map, and RBPDB) and SpliceAid v2 were used for evaluating SNPs in their capacity to alter motifs. By CRISPR/CAS9 mediated non-homologous end joining (NHEJ) these predictions were assessed experimentally using qPCR and Westen Blot. SNP rs5918762 was selected as it is in linkage disequilibrium with several PCa tagSNPs (rs5919393, rs5919432). rs5918762T/C is characterized by an unequal minor allele frequency (MAF) distribution among different populations. Using an in silico approach, this SNP is predicted to destroy/create a binding site for the splicing machinery involved protein SRSF9. Disrupting this SNP region via NHEJ resulted respectively in an increased and decreased expression of AR-FL and AR-V7 mRNA in 22RV1 cells (C allele). Additionally, analysis of the SU2C dataset (CRPC patients) correlated SRSF9 expression with AR-V7 expression. Subsequently, SRSF9 knock out (KO) resulted in reduced AR-V7 mRNA expression. Our data suggests that SNP rs5918762T/C is located in a region important for CE3 inclusion during AR splicing, which might involve SRSF9. Further validation of these results is in need and encompasses splicing assays by an AR-V7 mini-gene assay, protein-RNA interaction assays and an analysis of a lack of effect in cell lines expressing the T allele. Citation Format: Jasper Van Goubergen, Florian Handle, Marcus V. Cronauer, Frédéric R. Santer. Identification of functional single nucleotide polymorphisms in cryptic exon 3 of the androgen receptor gene [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2692.
Abstract 5098: Genetic and immunologic characteristics of biliary tract cancer patients with LRP1B mutation
Authors: Weiwei Chen, Hushan Zhang, Hongmin Dong, Gang Wang, Xiaokai Li, Wanghua Chen, Guodong Li, Saixi Bai, Juan Chen, Wenling Wang
Journal: Cancer Research (2022)

Abstract Background: Although the initial clinical results of immune checkpoint inhibitors (ICI) have been obtained in biliary tract cancer (BTC), and previous researches explored potential biomarkers for predicting response to ICI in BTC, and gene LRP1B was found as one of predictive biomarkers. Here we evaluated the mutation information of LRP1B in Chinese patients with BTC, and analyzed the potential explanation for more benefit from ICI treatment in patients with LRP1B mutation. Methods: The formalin-fixed paraffin-embedded specimens of 1324 cancer patients who have underwent next-generation sequencing (NGS) from 2016 to 2021, were included in this study. NGS was performed to detect gene mutation, and tumor mutational burden (TMB) measured by a 733 gene panel. PD-L1 expression detected by using Dako PD-L1 IHC 22C3 pharmDx. Result: The NGS results revealed that 12.76% (169/1324) patients with BTC have LRP1B mutation. Among these 1324 patients, 931 (patients with or without LRP1B mutations were 129 and 802, respectively) patients were available for analysis of TMB level, 820 ((patients with or without LRP1B mutations were 114 and 706, respectively)) patients for analysis of PD-L1 expression, and 1163 (patients with or without LRP1B mutations were 172 and 991, respectively) patients for analysis of MSI-H. TMB level and PD-L1 expression level were compared between groups with and without LRP1B mutation, and results showed that both these two biomarkers were higher in group with LRP1B mutation than without LRP1B mutation, especially TMB level was significantly higher (p&amp;lt;0.001).Further analysis revealed that the median TMB level, proportion of strong positive PD-L1 expression, and proportion of MSI-H were all higher in group of LRP1B mutation than wild type. Conclusion:These results suggest that LRP1B can be considered as one of effective biomarkers for ICI treatment in BTC, the underly mechanism may be related to the high TMB level. Citation Format: Weiwei Chen, Hushan Zhang, Hongmin Dong, Gang Wang, Xiaokai Li, Wanghua Chen, Guodong Li, Saixi Bai, Juan Chen, Wenling Wang. Genetic and immunologic characteristics of biliary tract cancer patients with LRP1B mutation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5098.
Abstract 5489: Utilization of cancer cell line screening and bioinformatic analyses to identify optimal developmental pathways for the novel anticancer agent BOLD-100
Authors: Paromita Raha, Brian Park, Adam Carie, Jim Pankovich, Mark Bazett
Journal: Cancer Research (2022)

Abstract Cell line screening of unique compounds can provide mechanistic insights and identify optimal drug combination partners. Bioinformatics analysis of cell screen data and correlation to publicly available datasets can support identification of appropriate patient populations for subsequent preclinical and clinical development. BOLD-100 is a first-in-class ruthenium-based anticancer agent currently being tested in a Phase 1b/2a clinical trial in combination with FOLFOX in the treatment of advanced gastrointestinal cancers. BOLD-100 works by altering the unfolded protein response through selective GRP78 inhibition; and inducing reactive oxygen species which causes DNA damage and cell cycle arrest. Collectively, these result in cell death in a range of different cancer types, and in combination with many different classes of anticancer agents. To determine optimal indications for BOLD-100 development, BOLD-100 was tested against 316 cancer cell lines in 72-hour Cell Titer Glo assays with downstream bioinformatic analysis and validation experiments. Multiple cancer types showed preferential response to BOLD-100, including bladder, esophageal, pancreatic, multiple myeloma and ovarian cancers. Subtype analysis identified potential populations of increased responsiveness, including in bladder cancer where BOLD-100 had increased response in luminal and mixed subtypes, as compared to basal subtypes. Utilizing bladder cancer as a case study, subsequent combination testing of BOLD-100 in combination with fluorouracil or cisplatin demonstrated that BOLD-100 enhanced cell death across different bladder cancer cell lines through synergistic interactions with these standard-of-care agents. The pan-cancer response profile of BOLD-100 was compared against 449 other anticancer drug responses that are part of the GDSC database. BOLD-100 displayed limited correlation with existing drugs, suggesting a unique mechanism of action and clinical utility where standard-of-care agents have limited efficacy. Pharmacogenomic analysis of the cell screen data indicated potential pathways and genes of relevance to BOLD-100 response, including increased response in KRAS-mutant cancers. Collectively, BOLD-100 showed a unique sensitivity profile across a panel of over 300 cancer cell lines, identifying multiple potential indications for future development. Subsequent investigations into several cancer types of interest and drug combinations are ongoing. Citation Format: Paromita Raha, Brian Park, Adam Carie, Jim Pankovich, Mark Bazett. Utilization of cancer cell line screening and bioinformatic analyses to identify optimal developmental pathways for the novel anticancer agent BOLD-100 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5489.
Abstract 1108: Evaluation of heme inhibitory therapy in combination with chemotherapy drugs on SCLC progression
Authors: Adnin Ashrafi, Narges Salamat, Li Zhang
Journal: Cancer Research (2022)

Abstract Lung cancer is the leading cause of cancer-related death in the US. It is mainly divided in two types: small cell lung cancer and non-small cell lung cancer. About 85-90% of cases are classified as non-small cell lung cancer (NSCLC). Small cell lung cancer (SCLC) is an aggressive neuroendocrine lung tumor representing 15% of lung cancers. Despite the advent of targeted therapies and chemotherapies, effective therapies for lung cancer are an unlikely outcome for most patients. SCLC is initially highly responsive to cisplatin and etoposide chemotherapy but, in almost every case, becomes rapidly chemo resistant. However, the mechanisms underlying initial sensitivity and subsequent resistance are not well investigated. Thus, alternative approaches and combination therapy is required for treating SCLCs. Recent studies in our lab show that NSCLC cells demonstrate elevated levels of heme via increased heme uptake and synthesis, and elevated oxidative phosphorylation (OXPHOS) and ATP generation which fuels NSCLC proliferation. Also, limiting heme via inhibition of heme uptake using heme sequestering peptides (HeSP2) can delay growth and progression of NSCLC tumors. This HeSP2 can also effectively inhibit angiogenesis, normalize tumor vasculature, and alleviate tumor hypoxia in NSCLC tumors and thereby inhibit lung tumor growth and progression. Tumor heterogeneity is critical for tumor growth, metastasis, and acquired therapeutic resistance. To understand if heme can effectively reduce tumor cell proliferation and growth and improve tumor microenvironment, we treated chemo resistant SCLCs with HeSP2 and in combination with commonly used chemo drugs cisplatin and etoposide. Our data shows that HesP2 can strongly inhibit cell proliferation and decreases oxygen consumption rate along with ATP generation in SCLCs. To gain insights into mechanism by which the heme sequestering peptides limit tumor growth and progression, we implanted subcutaneous or SCLC cell lines in NOD/SCID mice. Mice were treated with saline (control), HeSP2, HeSP2 and cisplatin, HeSP2 and etoposide. Tumor growth was monitored using caliper measurements. Tumors tissues were harvested, processed and paraffin embedded for immunohistochemistry (IHC) and histology experiments. These results indicate that heme sequestration can be a powerful strategy for suppressing lung tumors likely drug-resistant tumors that rely on oxidative phosphorylation for survival. Citation Format: Adnin Ashrafi, Narges Salamat, Li Zhang. Evaluation of heme inhibitory therapy in combination with chemotherapy drugs on SCLC progression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1108.
Abstract 321: Inhibition of CD39 results in elevated ATP and activation of myeloid cells to promote anti-tumor immunity
Authors: Christine E. Bowman, Ada Chen, Damie Juat, Kaustubh Parashar, Julie Clor, Hema Singh, Ritu Kushwaha, Bryan Handlos, Suan Liu, Janine Kline, Xiaoning Zhao, Hyock Joo Kwon, David Green, Stephen W. Young, Ester Fernandez-Salas, Matthew J. Walters, Nigel P. Walker
Journal: Cancer Research (2022)

Abstract CD39 (ENTPD1) is an ecto-nucleoside triphosphate diphosphohydrolase expressed widely in the tumor microenvironment (TME) responsible for catalyzing the conversion of ATP to AMP. Inhibition of CD39 enzymatic activity can promote anti-tumor immune responses by increasing the immunostimulatory substrate ATP and decreasing the formation of the product AMP, a precursor to immunoinhibitory adenosine. CD39 inhibition has been shown to have an anti-tumor effect by activating dendritic cells, macrophages, and NK cells in the TME to promote antigen presentation and inflammatory cytokine release. AB598 is a novel antibody, highly specific for human and cynomolgus CD39. AB598 potently binds to CD39 expressed on human primary myeloid cells and tumor cells and potently inhibits both soluble and membrane-bound CD39 enzymatic activity. CD39 inhibition results in increased extracellular ATP (eATP) in the TME and subsequent activation of P2X and P2Y receptors. Myeloid cells highly express both CD39 and P2X7, the P2X receptor with the weakest ligand affinity for ATP (greater than 100 μM), and most likely to be specifically activated by very high levels of eATP resulting from CD39 inhibition. Thus, the myeloid compartment has emerged as a key target associated with the therapeutic effects of CD39 inhibition. AB598 retains the ability to bind and inhibit membrane bound CD39 in the presence of high ATP (400 μM). AB598 promotes maturation of human dendritic cells in the presence of ATP, as determined by increased expression of CD83 and CD86 and decreased expression of CD14. In human macrophages treated with ATP, AB598 activates the inflammasome, resulting in the secretion of pro-inflammatory IL-18 and IL-1β. The ATP-dependent effects of AB598 support a therapeutic rationale of combining it with immunogenic therapies that induce release of ATP, such as chemotherapy and radiation, which might represent a new paradigm in the treatment of advanced solid tumors. Citation Format: Christine E. Bowman, Ada Chen, Damie Juat, Kaustubh Parashar, Julie Clor, Hema Singh, Ritu Kushwaha, Bryan Handlos, Suan Liu, Janine Kline, Xiaoning Zhao, Hyock Joo Kwon, David Green, Stephen W. Young, Ester Fernandez-Salas, Matthew J. Walters, Nigel P. Walker. Inhibition of CD39 results in elevated ATP and activation of myeloid cells to promote anti-tumor immunity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 321.
Abstract 3035: Proliferation induced by IL4R is regulated via Glut1 activity in metastatic breast cancer
Authors: Ebony Hargrove-Wiley, Daniel Valent, Demond Williams, Wendy Bindeman, Barbara Fingleton
Journal: Cancer Research (2022)

Abstract Metabolic reprogramming is a characteristic of all cancers including breast cancer; however, the signaling pathways involved are not fully understood. Altered metabolism, like a shift to aerobic glycolysis, supports cancer cell growth and metastatic behavior. Similarly, immune signals from the tumor microenvironment can promote these same phenotypes and therefore, immune signals likely influence the metabolic state of cancer cells. More specifically, the cytokine interleukin-4 (IL4) promotes increased tumor cell survival, proliferation, and invasion upon stimulation of the type II IL4 receptor alpha (IL4Rα) which is aberrantly expressed on epithelial cancer cells. Previously, we have shown that metastatic mouse mammary cancer cells (4T1) rely on IL4 signaling for colonization of metastatic sites in the lung and liver. Additionally, these cells uptake more glucose when treated with IL4 in vitro. Here, we investigated the significance of glucose consumption on pro-tumorigenic phenotypes induced by IL4/IL4Rα. In 4T1 cells, IL4/IL4Rα signaling increased protein expression and global glycosylation of a primary glucose transporter, Glut1. In human metastatic breast cancer cells (MDA-MB-231), CRISPR-mediated knockout (KO) of Glut1 significantly reduced basal and IL4-induced glucose consumption when assayed by 2-NBDG uptake, a fluorescently labeled glucose analog. Glut1 KO reversed the proliferative effects of IL4/IL4Rα activation on human cancer cells in vitro. Glut1 depletion attenuated tumor cell dependence on glucose consumption as shown by decreased expression of Hexokinase-2, a rate-limiting enzyme in glycolysis. In addition, KO cells have elevated levels of the glutamine transporter, ASCT2, that are further enhanced by IL4 treatment which suggest a greater reliance on glutamine albeit, insufficient for cell expansion supported by IL4/IL4Rα stimulation. Our data indicate that IL4-induced glucose consumption supports the increased metabolic activity necessary for cancer cell proliferation. Targeting the IL4/IL4Rα signaling axis could be a therapeutic strategy to hinder tumor-associated metabolism and reduce tumor burden at primary and metastatic sites. Citation Format: Ebony Hargrove-Wiley, Daniel Valent, Demond Williams, Wendy Bindeman, Barbara Fingleton. Proliferation induced by IL4R is regulated via Glut1 activity in metastatic breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3035.
Abstract 2409: EGFR-phosphorylated GDH1 harmonizes with RSK2 to drive CREB activation and tumor metastasis in EGFR mutated cancers
Authors: JiHoon Kang, Jung Seok Hwang, Austin Boese, Courteney Malin, Sumin Kang
Journal: Cancer Research (2022)

Abstract Cancer metastasis process involves dysregulated oncogenic kinase signaling, but the precise mechanism by which this orchestrates metabolic networks and signal cascades for metastasis is largely unclear. Here we report that pharmacological inhibition of a glutaminolytic enzyme glutamate dehydrogenase 1 (GDH1) and ribosomal S6 kinase 2 (RSK2) synergistically attenuates cell invasion, anoikis resistance, and immune escape more evidently in tumors harboring EGFR activating or EGFR inhibitor-resistant mutations. Mechanistically, GDH1 is activated by EGFR through phosphorylation at tyrosine 135, and together with RSK2 enhances transcriptional activity of CREB via CaMKIV signaling fostering metastasis. Moreover, GDH1, RSK2, and CREB phosphorylation positively correlate with EGFR mutation status and metastatic cancer progression in primary patient tumors. Our finding reveals a crosstalk between kinase, metabolic, and transcription machinery in metastasis and offers an alternative combinatorial therapeutic strategy to target EGFR therapy-resistant metastatic cancers. Citation Format: JiHoon Kang, Jung Seok Hwang, Austin Boese, Courteney Malin, Sumin Kang. EGFR-phosphorylated GDH1 harmonizes with RSK2 to drive CREB activation and tumor metastasis in EGFR mutated cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2409.